Preprint: Please note that this article has not completed peer review.

Identification of SNP Targeted Pathways From Genome-wide Association Study (GWAS) Data

Burcu Bakir-Gungor, Osman Ugur Sezerman
DOI: 10.21203/rs.2.1035/v2

Abstract

The identification of the variants that explain familial risk of a specific disease is important since it enables the development of genetic risk prediction tests, diagnosis tools and therapeutical applications. One possible reason of multifactorial diseases is the alterations in the activity of biological pathways, where a series of mutations occur in distinct genes. While each of these variations extends slightly the likelihood of having the disease, they work together to give birth to the perturbations in normal biological processes. We provide a protocol (termed PANOGA, Pathway and Network Oriented GWAS (Genome-wide association study) Analysis) to devise functionally important pathways through the identification of genes within these pathways, where these genes are targeted by single nucleotide polymorphisms (SNPs) obtained from the GWAS analysis. Additionally, PANOGA helps to identify other disease related genes, not targeted by the SNPs, which are also located within these affected pathways. The program accepts tab delimited or excel file containing SNP rsIDs vs. genotypic p-values and is available at: http://akademik.bahcesehir.edu.tr/~bbgungor/panoga_protocol.zip

Keywords
Genome-wide association study, GWAS, human complex disease, single nucleotide polymorphism, SNP, pathway, protein protein interaction network, SNP functional information

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Preprint: Please note that this article has not completed peer review.

Identification of SNP Targeted Pathways From Genome-wide Association Study (GWAS) Data

Burcu Bakir-Gungor, Osman Ugur Sezerman

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Abstract

The identification of the variants that explain familial risk of a specific disease is important since it enables the development of genetic risk prediction tests, diagnosis tools and therapeutical applications. One possible reason of multifactorial diseases is the alterations in the activity of biological pathways, where a series of mutations occur in distinct genes. While each of these variations extends slightly the likelihood of having the disease, they work together to give birth to the perturbations in normal biological processes. We provide a protocol (termed PANOGA, Pathway and Network Oriented GWAS (Genome-wide association study) Analysis) to devise functionally important pathways through the identification of genes within these pathways, where these genes are targeted by single nucleotide polymorphisms (SNPs) obtained from the GWAS analysis. Additionally, PANOGA helps to identify other disease related genes, not targeted by the SNPs, which are also located within these affected pathways. The program accepts tab delimited or excel file containing SNP rsIDs vs. genotypic p-values and is available at: http://akademik.bahcesehir.edu.tr/~bbgungor/panoga_protocol.zip

Figures

Introduction

Equipment

Procedure

Timing

Troubleshooting

Anticipated Results

References

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